MCID: SPC026
MIFTS: 27

Specific Granule Deficiency 1

Categories: Genetic diseases

Aliases & Classifications for Specific Granule Deficiency 1

MalaCards integrated aliases for Specific Granule Deficiency 1:

Name: Specific Granule Deficiency 1 57 75
Specific Granule Deficiency 57 29 13 55 6 40 73
Sgd1 57 75
Lactoferrin-Deficient Neutrophils 57
Neutrophil Lactoferrin Deficiency 57

Characteristics:

OMIM:

57
Inheritance:
autosomal recessive


HPO:

32
specific granule deficiency 1:
Inheritance autosomal recessive inheritance


Classifications:



External Ids:

OMIM 57 245480
MedGen 42 C0398593
MeSH 44 D007960
SNOMED-CT via HPO 69 258211005 85559002
UMLS 73 C0398593

Summaries for Specific Granule Deficiency 1

UniProtKB/Swiss-Prot : 75 Specific granule deficiency 1: An autosomal recessive disorder characterized by recurrent pyogenic infections, defective neutrophil chemotaxis and bactericidal activity, and lack of neutrophil secondary granule proteins. Neutrophils of affected individuals lack lactoferrin and show abnormal nuclear segmentation, bilobed nuclei, low alkaline phosphatase, and increased number of neutrophil mitochondria and ribosomes.

MalaCards based summary : Specific Granule Deficiency 1, also known as specific granule deficiency, is related to neutrophil-specific granule deficiency and specific granule deficiency 2. An important gene associated with Specific Granule Deficiency 1 is CEBPE (CCAAT Enhancer Binding Protein Epsilon). Affiliated tissues include neutrophil, monocytes and myeloid, and related phenotypes are recurrent infections and hyposegmentation of neutrophil nuclei

Description from OMIM: 245480

Related Diseases for Specific Granule Deficiency 1

Diseases related to Specific Granule Deficiency 1 via text searches within MalaCards or GeneCards Suite gene sharing:

# Related Disease Score Top Affiliating Genes
1 neutrophil-specific granule deficiency 30.3 CEBPE SMARCD2
2 specific granule deficiency 2 11.0

Symptoms & Phenotypes for Specific Granule Deficiency 1

Symptoms via clinical synopsis from OMIM:

57
Misc:
recurrent infections

Lab:
absent neutrophil specific granules
absent neutrophil lactoferrin
abnormal neutrophil nuclear segmentation
neutrophil nuclear clefts
low neutrophil alkaline phosphatase
more

Clinical features from OMIM:

245480

Human phenotypes related to Specific Granule Deficiency 1:

32
# Description HPO Frequency HPO Source Accession
1 recurrent infections 32 HP:0002719
2 hyposegmentation of neutrophil nuclei 32 HP:0011447
3 absent neutrophil specific granules 32 HP:0012551

Drugs & Therapeutics for Specific Granule Deficiency 1

Interventional clinical trials:


# Name Status NCT ID Phase Drugs
1 Trial to Incentivise Adherence for Diabetes Active, not recruiting NCT02224417 Not Applicable

Search NIH Clinical Center for Specific Granule Deficiency 1

Genetic Tests for Specific Granule Deficiency 1

Genetic tests related to Specific Granule Deficiency 1:

# Genetic test Affiliating Genes
1 Specific Granule Deficiency 29 CEBPE

Anatomical Context for Specific Granule Deficiency 1

MalaCards organs/tissues related to Specific Granule Deficiency 1:

41
Neutrophil, Monocytes, Myeloid, Testes

Publications for Specific Granule Deficiency 1

Articles related to Specific Granule Deficiency 1:

(show all 19)
# Title Authors Year
1
Role of the Leucine Zipper Domain of CCAAT/ Enhancer Binding Protein-Epsilon (C/EBPI/) in Neutrophil-Specific Granule Deficiency. ( 28322138 )
2016
2
A Novel In-Frame Deletion in the Leucine Zipper Domain of C/EBPI/ Leads to Neutrophil-Specific Granule Deficiency. ( 26019275 )
2015
3
Clinical course in a patient with neutrophil-specific granule deficiency and rapid detection of neutrophil granules as a screening test. ( 25081842 )
2014
4
Neutrophil-specific granule deficiency. ( 23294125 )
2013
5
Growth factor independence-1 (Gfi-1) plays a role in mediating specific granule deficiency (SGD) in a patient lacking a gene-inactivating mutation in the C/EBPepsilon gene. ( 17244686 )
2007
6
Intractable diarrhoea of infancy caused by neutrophil specific granule deficiency and cured by stem cell transplantation. ( 16407388 )
2006
7
Aberrant expression of neutrophil and macrophage-related genes in a murine model for human neutrophil-specific granule deficiency. ( 16204633 )
2005
8
Phenotypic and functional alterations of peripheral blood monocytes in neutrophil-specific granule deficiency. ( 14576362 )
2004
9
Neutrophil specific granule deficiency and mutations in the gene encoding transcription factor C/EBP(epsilon). ( 11753076 )
2002
10
Neutrophil-specific granule deficiency: homozygous recessive inheritance of a frameshift mutation in the gene encoding transcription factor CCAAT/enhancer binding protein--epsilon. ( 11313242 )
2001
11
Neutrophil-specific granule deficiency results from a novel mutation with loss of function of the transcription factor CCAAT/enhancer binding protein epsilon. ( 10359588 )
1999
12
A marked decrease in defensin mRNA in the only case of congenital neutrophil-specific granule deficiency reported in Japan. ( 8018907 )
1994
13
Ultrastructure of neutrophilic phagosome of autologous platelet in vivo in specific granule deficiency. ( 8342544 )
1993
14
Neutrophil-specific granule deficiency includes eosinophils. ( 8324226 )
1993
15
Correlation of messenger RNA levels with protein defects in specific granule deficiency. ( 1327289 )
1992
16
Selective defect in myeloid cell lactoferrin gene expression in neutrophil specific granule deficiency. ( 2536400 )
1989
17
Endogenous inhibitor of protein kinase C: association with human peripheral blood neutrophils but not with specific granule-deficient neutrophils or cytoplasts. ( 3462245 )
1986
18
Neutrophil specific granule deficiency. ( 3888052 )
1985
19
Human neutrophil-specific granule deficiency: a model to assess the role of neutrophil-specific granules in the evolution of the inflammatory response. ( 7044447 )
1982

Variations for Specific Granule Deficiency 1

ClinVar genetic disease variations for Specific Granule Deficiency 1:

6
(show all 26)
# Gene Variation Type Significance SNP ID Assembly Location
1 CEBPE CEBPE, 5-BP DEL, NT224 deletion Pathogenic
2 CEBPE CEBPE, 1-BP INS, 1113A insertion Pathogenic
3 SMARCD2 NM_001098426.1(SMARCD2): c.1181+1G> A single nucleotide variant Pathogenic rs1057518731 GRCh37 Chromosome 17, 61911268: 61911268
4 SMARCD2 NM_001098426.1(SMARCD2): c.1181+1G> A single nucleotide variant Pathogenic rs1057518731 GRCh38 Chromosome 17, 63833908: 63833908
5 SMARCD2 NM_001098426.1(SMARCD2): c.414_438dup25 (p.Gln147Glufs) duplication Pathogenic rs1057518732 GRCh37 Chromosome 17, 61914561: 61914585
6 SMARCD2 NM_001098426.1(SMARCD2): c.414_438dup25 (p.Gln147Glufs) duplication Pathogenic rs1057518732 GRCh38 Chromosome 17, 63837201: 63837225
7 SMARCD2 NM_001098426.1(SMARCD2): c.401+2T> C single nucleotide variant Pathogenic rs1057518733 GRCh38 Chromosome 17, 63837439: 63837439
8 SMARCD2 NM_001098426.1(SMARCD2): c.401+2T> C single nucleotide variant Pathogenic rs1057518733 GRCh37 Chromosome 17, 61914799: 61914799
9 CEBPE NM_001805.3(CEBPE): c.496C> G (p.Leu166Val) single nucleotide variant Uncertain significance GRCh37 Chromosome 14, 23587805: 23587805
10 CEBPE NM_001805.3(CEBPE): c.496C> G (p.Leu166Val) single nucleotide variant Uncertain significance GRCh38 Chromosome 14, 23118596: 23118596
11 CEBPE NM_001805.3(CEBPE): c.303G> A (p.Ala101=) single nucleotide variant Likely benign rs149752323 GRCh37 Chromosome 14, 23587998: 23587998
12 CEBPE NM_001805.3(CEBPE): c.303G> A (p.Ala101=) single nucleotide variant Likely benign rs149752323 GRCh38 Chromosome 14, 23118789: 23118789
13 CEBPE NM_001805.3(CEBPE): c.747C> T (p.Arg249=) single nucleotide variant Benign rs55722931 GRCh37 Chromosome 14, 23586795: 23586795
14 CEBPE NM_001805.3(CEBPE): c.747C> T (p.Arg249=) single nucleotide variant Benign rs55722931 GRCh38 Chromosome 14, 23117586: 23117586
15 CEBPE NM_001805.3(CEBPE): c.487G> A (p.Gly163Ser) single nucleotide variant Uncertain significance rs762842144 GRCh38 Chromosome 14, 23118605: 23118605
16 CEBPE NM_001805.3(CEBPE): c.487G> A (p.Gly163Ser) single nucleotide variant Uncertain significance rs762842144 GRCh37 Chromosome 14, 23587814: 23587814
17 CEBPE NM_001805.3(CEBPE): c.234C> T (p.Pro78=) single nucleotide variant Benign rs114913626 GRCh38 Chromosome 14, 23118858: 23118858
18 CEBPE NM_001805.3(CEBPE): c.234C> T (p.Pro78=) single nucleotide variant Benign rs114913626 GRCh37 Chromosome 14, 23588067: 23588067
19 CEBPE NM_001805.3(CEBPE): c.205C> T (p.Leu69Phe) single nucleotide variant Uncertain significance rs146580935 GRCh37 Chromosome 14, 23588096: 23588096
20 CEBPE NM_001805.3(CEBPE): c.205C> T (p.Leu69Phe) single nucleotide variant Uncertain significance rs146580935 GRCh38 Chromosome 14, 23118887: 23118887
21 CEBPE NM_001805.3(CEBPE): c.463C> A (p.Leu155Met) single nucleotide variant Benign rs141903485 GRCh37 Chromosome 14, 23587838: 23587838
22 CEBPE NM_001805.3(CEBPE): c.463C> A (p.Leu155Met) single nucleotide variant Benign rs141903485 GRCh38 Chromosome 14, 23118629: 23118629
23 CEBPE NM_001805.3(CEBPE): c.391C> T (p.Arg131Ter) single nucleotide variant Pathogenic rs760325316 GRCh37 Chromosome 14, 23587910: 23587910
24 CEBPE NM_001805.3(CEBPE): c.391C> T (p.Arg131Ter) single nucleotide variant Pathogenic rs760325316 GRCh38 Chromosome 14, 23118701: 23118701
25 CEBPE NM_001805.3(CEBPE): c.357G> T (p.Ala119=) single nucleotide variant Likely benign rs202220573 GRCh37 Chromosome 14, 23587944: 23587944
26 CEBPE NM_001805.3(CEBPE): c.357G> T (p.Ala119=) single nucleotide variant Likely benign rs202220573 GRCh38 Chromosome 14, 23118735: 23118735

Expression for Specific Granule Deficiency 1

Search GEO for disease gene expression data for Specific Granule Deficiency 1.

Pathways for Specific Granule Deficiency 1

GO Terms for Specific Granule Deficiency 1

Cellular components related to Specific Granule Deficiency 1 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 protein-containing complex GO:0032991 8.62 LTF SMARCD2

Biological processes related to Specific Granule Deficiency 1 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 regulation of transcription, DNA-templated GO:0006355 9.33 CEBPE LTF SMARCD2
2 transcription, DNA-templated GO:0006351 9.13 CEBPE LTF SMARCD2
3 defense response to bacterium GO:0042742 8.62 CEBPE LTF

Molecular functions related to Specific Granule Deficiency 1 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 RNA polymerase II proximal promoter sequence-specific DNA binding GO:0000978 8.62 CEBPE SMARCD2

Sources for Specific Granule Deficiency 1

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
17 ExPASy
19 FMA
28 GO
29 GTR
30 HGMD
31 HMDB
32 HPO
33 ICD10
34 ICD10 via Orphanet
35 ICD9CM
36 IUPHAR
37 KEGG
38 LifeMap
40 LOVD
42 MedGen
44 MeSH
45 MESH via Orphanet
46 MGI
49 NCI
50 NCIt
51 NDF-RT
54 NINDS
55 Novoseek
57 OMIM
58 OMIM via Orphanet
62 PubMed
64 QIAGEN
69 SNOMED-CT via HPO
70 SNOMED-CT via Orphanet
71 TGDB
72 Tocris
73 UMLS
74 UMLS via Orphanet
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